In certain DNA sequencing systems, identities of nucleotides of a sample can be determined by identifying complementary nucleotides that hybridize to or pair or otherwise match with nucleotides of the sample. One or more of such complementary nucleotides may be part of a probe or probe set that can be used to test or interrogate the sample nucleotide sequence.
Typically, probes include a detectable feature such as chemical or physical features that can be identified under suitable conditions. As an example, dyes that fluoresce or otherwise emit an optical signal under suitable conditions can be used as detectable features. By detecting the feature (e.g., the fluorescence of a dye), information about the probe, and thus the portion of the sample where the probe hybridizes, pairs, or matches can be obtained.
Errors and ambiguities can be introduced or otherwise occur at or during various stages of sequencing and sequencing-related operations and processes. In certain situations, it can be impossible to even know that an error has occurred or an ambiguity exists. While it may in some situations be possible to resolve ambiguity or distinguish an error from correct but unusual or unexpected sequence information such as single nucleotide polymorphism, determining whether the sequence information is ambiguous, correct, or erroneous can typically only be detected by comparison of the sequence information with a reference. Further, even if the putative sequencing error or ambiguity is identified as a true error or ambiguity, there is often no mechanism or capability to correct the error or ambiguity without having to repeat some or all of the measurements.